Background: In heavily endemic malaria areas, it is almost inevitable that malarial infection will be associated with anaemia, although malaria may not be the prime cause of it. Anaemia is a major public health problem in Cameroon. We hypothesized that, factors other than falciparum malaria account for anaemia in the study area. Methods: A longitudinal study was conducted among 351 Plasmodium falciparum positive children to determine the prevalence, risk factors and the perception of anaemia by the caregivers in a semi-rural community. The investigative methods included the use of a structured questionnaire, clinical evaluation and laboratory investigations. Results: At enrolment the overall prevalence of anaemia as assessed by Hb concentration (Hb < 11 g/dl) was 80.3% (282). Following treatment the prevalence of persistent anaemia was 6% and 46.2% of the children achieved haematological recovery by day 42. Exploratory multiple linear regression analysis showed the following; parasitaemia density (P < 0.01), enlarged spleen (P < 0.05), duration of fever > 2 days (P < 0.01), high white blood cell count (P < 0.001), sex (P < 0.05), iron status indicators (ferritin and transferrin) (P < 0.001), level of education of the caregiver (P < 0.05), management of onset of malaria by caregiver (P < 0.005) and wasting (P < 0.05) to be risk factors for anaemia in children with falciparum infection. Approximately 75.5% (265) of the caregivers had some knowledge about anaemia. Conclusion: The identified risk factors revealed the important contributors to the pathogenesis of anaemia in the Mount Cameroon region. Control efforts should therefore be directed towards proper health education emphasizing on proper health seeking behaviour and attitudes of the population.